Suppr超能文献

利用基因组关系矩阵降低限制最大似然估计的计算需求。

Reducing computational demands of restricted maximum likelihood estimation with genomic relationship matrices.

机构信息

AGBU, A Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW, 2351, Australia.

出版信息

Genet Sel Evol. 2023 Jan 25;55(1):7. doi: 10.1186/s12711-023-00781-7.

Abstract

Restricted maximum likelihood estimation of genetic parameters accounting for genomic relationships has been reported to impose computational burdens which typically are many times higher than those of corresponding analyses considering pedigree based relationships only. This can be attributed to the dense nature of genomic relationship matrices and their inverses. We outline a reparameterisation of the multivariate linear mixed model to principal components and its effects on the sparsity pattern of the pertaining coefficient matrix in the mixed model equations. Using two data sets we demonstrate that this can dramatically reduce the computing time per iterate of the widely used 'average information' algorithm for restricted maximum likelihood. This is primarily due to the fact that on the principal component scale, the first derivatives of the coefficient matrix with respect to the parameters modelling genetic covariances between traits are independent of the relationship matrix between individuals, i.e. are not afflicted by a multitude of genomic relationships.

摘要

已有研究报告称,考虑到基因组关系,对遗传参数进行限制最大似然估计会带来计算负担,通常比仅考虑基于系谱关系的分析高出许多倍。这归因于基因组关系矩阵及其逆的密集性质。我们概述了多元线性混合模型向主成分的重新参数化及其对混合模型方程中相关系数矩阵稀疏模式的影响。使用两个数据集,我们证明这可以极大地减少广泛使用的“平均信息”算法对限制最大似然的每次迭代的计算时间。这主要是因为在主成分尺度上,关于性状间遗传协方差建模的参数的系数矩阵的一阶导数与个体之间的关系矩阵无关,即不受众多基因组关系的影响。

相似文献

2
Restricted maximum likelihood estimation of genetic principal components and smoothed covariance matrices.
Genet Sel Evol. 2005 Jan-Feb;37(1):1-30. doi: 10.1186/1297-9686-37-1-1.
4
Technical note: Automatic scaling in single-step genomic BLUP.
J Dairy Sci. 2021 Feb;104(2):2027-2031. doi: 10.3168/jds.2020-18969. Epub 2020 Dec 11.
6
Solving efficiently large single-step genomic best linear unbiased prediction models.
J Anim Breed Genet. 2017 Jun;134(3):264-274. doi: 10.1111/jbg.12257.
7
Genomic prediction of breeding values in the New Zealand sheep industry using a 50K SNP chip.
J Anim Sci. 2014 Oct;92(10):4375-89. doi: 10.2527/jas.2014-7801. Epub 2014 Aug 22.
8
Metafounders are related to F fixation indices and reduce bias in single-step genomic evaluations.
Genet Sel Evol. 2017 Mar 10;49(1):34. doi: 10.1186/s12711-017-0309-2.
9
Genomic Model with Correlation Between Additive and Dominance Effects.
Genetics. 2018 Jul;209(3):711-723. doi: 10.1534/genetics.118.301015. Epub 2018 May 9.
10
On the distance of genetic relationships and the accuracy of genomic prediction in pig breeding.
Genet Sel Evol. 2014 Aug 1;46(1):49. doi: 10.1186/1297-9686-46-49.

引用本文的文献

本文引用的文献

2
Current status of genomic evaluation.
J Anim Sci. 2020 Apr 1;98(4). doi: 10.1093/jas/skaa101.
3
AlphaSim: Software for Breeding Program Simulation.
Plant Genome. 2016 Nov;9(3). doi: 10.3835/plantgenome2016.02.0013.
4
MTG2: an efficient algorithm for multivariate linear mixed model analysis based on genomic information.
Bioinformatics. 2016 May 1;32(9):1420-2. doi: 10.1093/bioinformatics/btw012. Epub 2016 Jan 10.
8
Using recursion to compute the inverse of the genomic relationship matrix.
J Dairy Sci. 2014;97(6):3943-52. doi: 10.3168/jds.2013-7752. Epub 2014 Mar 27.
9
Bias in genomic predictions for populations under selection.
Genet Res (Camb). 2011 Oct;93(5):357-66. doi: 10.1017/S001667231100022X. Epub 2011 Jul 18.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验